drseqFilter: Screen SURF training samples

Description Usage Arguments Value

View source: R/estimate.R

Description

Filter DrSeq results for the analysis module 2 of SURF (DASeq).

Usage

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drseqFilter(
  event,
  drseq.fdr = 0.05,
  read.length = 100,
  min.adjMean = 0.05,
  filter.overlap.event = TRUE,
  verbose = FALSE
)

Arguments

event

a surf object output by drseqFit.

drseq.fdr

numeric, FDR (BH procedure) adjusted p-value cut-off.

read.length

numeric, RNA-seq read length. Default is 100 bp (e.g., Illumina TruSeq). This is used to adjust event base count, which is then used to select the representative events if replicated.

min.adjMean

numeric, adjusted event base mean threshold.

filter.overlap.event

logical, whether (default to TRUE) to select one representitive event from overlapping ones and remove the others.

verbose

logical, whether (default to FALSE) to print out basic summary statistics.

Value

a surf object, with three columns added:

adjMean

adjusted base mean of the event from RNA-seq data.

group

group labels of ATR events, increase for increased REU upon RBP knock-down, and decrease for decreased, and no change for no-changed.

included

logical, indicating whether the event is included into SURF analysis module 2.


fchen365/surf documentation built on June 18, 2021, 12:02 p.m.